I feel right now like there are very limited ways of obtaining Fleet Marks (not so much Dilithium, but other options are always great) in STO, so I'm gonna cut to the chase and throw some ideas out there.
I really like the featured episodes and replay them more than any other missions. Why not give VAs Fleet Marks and/or Dilithium for playing them, in place of skill points? Something like X Expertise with a choice between 15 Fleet Marks per mission OR 480 Dilithium per mission.
I love these. They're like mini-Fleet Actions, purely space combat, great for soloing (and we'd all love a little with that seeing how much dead weight there can be in a fleet action).
Instead of rewarding us with Skill Points for completing a patrol at VA, reward us 10 Fleet Marks OR the choice of 480(?) Dilithium.
Give us a Daily/Repeatable mission to explore 2 or 3 systems at a time, that we can turn in for 1440 Dilithium OR 30 Fleet Marks.
Something that would also be great, especially for something like the "Investigate Officer Reports" mission, is to instead give players X SKILL POINTS, X EXPERTISE, 960 DILITHIUM and then give them a choice between 50 FLEET MARKS or ANOTHER 960 DILITHIUM (Totalling 1920). This would help out people not in a fleet who want to grind for extra Dilithium.
More anything? "MORE EVERYTHING!"
-Jerry Seinfeld on Star Trek Online Content